I managed to get around the unchecking thing by selecting "control from here" for the capsule of the ship that carries the experiment, so after undocking it remains active. This way, the objective does not uncheck, but after returning the experiment to Kerbin, the contract does not complete. I recover the capsule and the part with the experiment, and the contract reverts to all objectives unchecked. I installed it from CKAN, I can try to remove it and install the github version, in case that they are not the same.
About the debug, I'm not sure how I should use it. Thank you for your help, by the way.